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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.23

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-07-30, 00:44 EEST based on data in: /wrk-vakka/users/nikiarte/rnaseq_analysis/snakemake/fastqc_notrim


        General Statistics

        Showing 138/138 rows and 4/6 columns.
        Sample Name% Dups% GCMedian Read LengthM Seqs
        SRR14240730_1
        72.0%
        50%
        142bp
        79.1M
        SRR14240730_2
        66.3%
        51%
        147bp
        79.1M
        SRR14240731_1
        66.2%
        48%
        147bp
        97.2M
        SRR14240731_2
        60.6%
        48%
        147bp
        97.2M
        SRR14240732_1
        62.7%
        46%
        137bp
        80.7M
        SRR14240732_2
        55.8%
        47%
        142bp
        80.7M
        SRR14240733_1
        61.0%
        47%
        147bp
        66.4M
        SRR14240733_2
        52.3%
        47%
        147bp
        66.4M
        SRR14240734_1
        74.3%
        49%
        142bp
        132.6M
        SRR14240734_2
        68.7%
        50%
        142bp
        132.6M
        SRR14240735_1
        66.8%
        49%
        142bp
        141.6M
        SRR14240735_2
        60.7%
        50%
        147bp
        141.6M
        SRR14240736_1
        73.8%
        51%
        137bp
        95.1M
        SRR14240736_2
        68.4%
        52%
        142bp
        95.1M
        SRR14240737_1
        73.9%
        50%
        137bp
        111.1M
        SRR14240737_2
        68.3%
        51%
        142bp
        111.1M
        SRR14240738_1
        68.4%
        48%
        142bp
        113.3M
        SRR14240738_2
        60.6%
        49%
        147bp
        113.3M
        SRR14240739_1
        76.1%
        51%
        137bp
        89.7M
        SRR14240739_2
        71.4%
        51%
        142bp
        89.7M
        SRR14240740_1
        71.2%
        50%
        137bp
        100.1M
        SRR14240740_2
        66.4%
        51%
        137bp
        100.1M
        SRR14240741_1
        66.2%
        46%
        137bp
        94.6M
        SRR14240741_2
        56.7%
        47%
        142bp
        94.6M
        SRR14240742_1
        47.2%
        46%
        151bp
        41.6M
        SRR14240742_2
        39.6%
        46%
        151bp
        41.6M
        SRR14240743_1
        67.4%
        53%
        142bp
        66.7M
        SRR14240743_2
        62.9%
        53%
        142bp
        66.7M
        SRR14240744_1
        65.2%
        49%
        137bp
        114.2M
        SRR14240744_2
        59.3%
        49%
        142bp
        114.2M
        SRR14240745_1
        63.1%
        48%
        142bp
        77.6M
        SRR14240745_2
        55.6%
        49%
        147bp
        77.6M
        SRR14240746_1
        71.1%
        51%
        142bp
        98.5M
        SRR14240746_2
        66.7%
        52%
        142bp
        98.5M
        SRR14240747_1
        60.7%
        46%
        147bp
        73.5M
        SRR14240747_2
        52.5%
        47%
        147bp
        73.5M
        SRR14240748_1
        68.7%
        49%
        137bp
        95.8M
        SRR14240748_2
        62.4%
        50%
        142bp
        95.8M
        SRR14240749_1
        68.8%
        46%
        142bp
        97.3M
        SRR14240749_2
        61.4%
        46%
        147bp
        97.3M
        SRR14240750_1
        68.5%
        48%
        142bp
        86.2M
        SRR14240750_2
        61.3%
        48%
        142bp
        86.2M
        SRR14240751_1
        84.3%
        50%
        127bp
        75.7M
        SRR14240751_2
        76.2%
        52%
        137bp
        75.7M
        SRR14240752_1
        65.7%
        48%
        151bp
        69.6M
        SRR14240752_2
        58.9%
        49%
        151bp
        69.6M
        SRR14240753_1
        59.0%
        46%
        137bp
        97.4M
        SRR14240753_2
        49.9%
        46%
        142bp
        97.4M
        SRR14240754_1
        61.8%
        50%
        137bp
        60.9M
        SRR14240754_2
        51.1%
        52%
        142bp
        60.9M
        SRR14240755_1
        61.0%
        48%
        142bp
        85.7M
        SRR14240755_2
        53.6%
        48%
        142bp
        85.7M
        SRR14240756_1
        57.5%
        49%
        132bp
        56.4M
        SRR14240756_2
        48.2%
        50%
        137bp
        56.4M
        SRR14240757_1
        72.8%
        51%
        137bp
        79.8M
        SRR14240757_2
        62.9%
        52%
        147bp
        79.8M
        SRR14240758_1
        58.8%
        47%
        151bp
        55.6M
        SRR14240758_2
        50.1%
        47%
        151bp
        55.6M
        SRR14240759_1
        50.2%
        47%
        147bp
        45.2M
        SRR14240759_2
        40.9%
        47%
        147bp
        45.2M
        SRR14240760_1
        61.9%
        48%
        151bp
        102.3M
        SRR14240760_2
        54.0%
        48%
        151bp
        102.3M
        SRR14240761_1
        76.6%
        49%
        137bp
        71.0M
        SRR14240761_2
        65.9%
        51%
        147bp
        71.0M
        SRR14240762_1
        64.5%
        48%
        137bp
        154.2M
        SRR14240762_2
        56.5%
        48%
        142bp
        154.2M
        SRR14240763_1
        55.5%
        48%
        147bp
        68.7M
        SRR14240763_2
        46.3%
        49%
        151bp
        68.7M
        SRR14240764_1
        60.7%
        45%
        137bp
        87.8M
        SRR14240764_2
        51.5%
        47%
        142bp
        87.8M
        SRR14240765_1
        66.8%
        48%
        142bp
        125.1M
        SRR14240765_2
        58.0%
        49%
        147bp
        125.1M
        SRR14240766_1
        63.8%
        48%
        137bp
        87.3M
        SRR14240766_2
        57.4%
        48%
        142bp
        87.3M
        SRR14240767_1
        56.6%
        46%
        147bp
        85.4M
        SRR14240767_2
        46.9%
        46%
        147bp
        85.4M
        SRR14240768_1
        60.2%
        48%
        147bp
        59.7M
        SRR14240768_2
        50.3%
        49%
        147bp
        59.7M
        SRR14240769_1
        63.0%
        48%
        142bp
        119.3M
        SRR14240769_2
        53.4%
        48%
        147bp
        119.3M
        SRR14240770_1
        69.7%
        46%
        137bp
        85.2M
        SRR14240770_2
        59.9%
        47%
        142bp
        85.2M
        SRR14240771_1
        64.9%
        47%
        147bp
        66.8M
        SRR14240771_2
        58.5%
        48%
        151bp
        66.8M
        SRR14240772_1
        67.5%
        50%
        142bp
        86.5M
        SRR14240772_2
        58.1%
        51%
        147bp
        86.5M
        SRR14240773_1
        57.4%
        47%
        142bp
        88.2M
        SRR14240773_2
        46.9%
        48%
        147bp
        88.2M
        SRR14240774_1
        57.0%
        50%
        147bp
        27.4M
        SRR14240774_2
        50.6%
        50%
        147bp
        27.4M
        SRR14240775_1
        67.4%
        51%
        137bp
        126.2M
        SRR14240775_2
        59.5%
        51%
        142bp
        126.2M
        SRR14240776_1
        54.5%
        48%
        137bp
        97.2M
        SRR14240776_2
        46.9%
        48%
        142bp
        97.2M
        SRR14240777_1
        57.9%
        49%
        142bp
        86.1M
        SRR14240777_2
        51.0%
        49%
        142bp
        86.1M
        SRR14240778_1
        60.2%
        48%
        142bp
        90.3M
        SRR14240778_2
        51.8%
        49%
        147bp
        90.3M
        SRR14240779_1
        65.6%
        50%
        142bp
        122.3M
        SRR14240779_2
        58.1%
        50%
        142bp
        122.3M
        SRR14240780_1
        65.6%
        48%
        142bp
        115.1M
        SRR14240780_2
        54.7%
        49%
        147bp
        115.1M
        SRR14240781_1
        65.2%
        49%
        137bp
        76.6M
        SRR14240781_2
        56.8%
        50%
        142bp
        76.6M
        SRR14240782_1
        68.7%
        48%
        142bp
        79.8M
        SRR14240782_2
        61.3%
        49%
        147bp
        79.8M
        SRR14240783_1
        59.8%
        46%
        142bp
        82.8M
        SRR14240783_2
        52.6%
        47%
        142bp
        82.8M
        SRR14240784_1
        67.5%
        48%
        151bp
        94.4M
        SRR14240784_2
        59.6%
        49%
        151bp
        94.4M
        SRR14240785_1
        67.3%
        53%
        127bp
        76.7M
        SRR14240785_2
        57.8%
        56%
        142bp
        76.7M
        SRR14240786_1
        63.3%
        46%
        147bp
        104.0M
        SRR14240786_2
        55.1%
        46%
        147bp
        104.0M
        SRR14240787_1
        66.3%
        47%
        147bp
        118.1M
        SRR14240787_2
        57.0%
        48%
        147bp
        118.1M
        SRR14240788_1
        67.4%
        50%
        137bp
        58.7M
        SRR14240788_2
        59.3%
        51%
        142bp
        58.7M
        SRR14240789_1
        78.6%
        56%
        132bp
        90.8M
        SRR14240789_2
        72.5%
        58%
        137bp
        90.8M
        SRR14240790_1
        64.9%
        47%
        142bp
        74.0M
        SRR14240790_2
        56.1%
        48%
        142bp
        74.0M
        SRR14240791_1
        70.7%
        48%
        142bp
        100.7M
        SRR14240791_2
        61.4%
        49%
        147bp
        100.7M
        SRR14240792_1
        68.4%
        46%
        127bp
        78.0M
        SRR14240792_2
        52.7%
        50%
        147bp
        78.0M
        SRR14240793_1
        61.2%
        49%
        137bp
        160.2M
        SRR14240793_2
        52.4%
        49%
        142bp
        160.2M
        SRR14240794_1
        68.6%
        52%
        127bp
        65.1M
        SRR14240794_2
        58.3%
        55%
        137bp
        65.1M
        SRR14240795_1
        72.5%
        50%
        147bp
        100.3M
        SRR14240795_2
        66.5%
        51%
        147bp
        100.3M
        SRR14240796_1
        62.1%
        49%
        137bp
        88.1M
        SRR14240796_2
        55.3%
        49%
        142bp
        88.1M
        SRR14240797_1
        71.1%
        49%
        142bp
        141.1M
        SRR14240797_2
        63.0%
        50%
        142bp
        141.1M
        SRR14240798_1
        58.3%
        49%
        147bp
        89.7M
        SRR14240798_2
        50.7%
        50%
        147bp
        89.7M

        FastQC

        Version: 0.12.1

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 20/20 rows and 3/3 columns.
        Overrepresented sequenceSamplesOccurrences% of all reads
        CCCGTCCCGGGGGTTGGCCGCGCGGGCCCCGGTGGGGCGGCCACCCGGGG
        88
        15801227
        0.1272%
        NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
        72
        117867077
        0.9489%
        CCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATG
        69
        103650481
        0.8345%
        CCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATAT
        69
        47547799
        0.3828%
        CTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGC
        69
        55391491
        0.4460%
        CCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATT
        69
        46291772
        0.3727%
        CTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT
        69
        29533395
        0.2378%
        CTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGA
        69
        45347008
        0.3651%
        CCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTG
        69
        38102779
        0.3068%
        CTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACCTT
        69
        29830367
        0.2402%
        GCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGG
        69
        15716569
        0.1265%
        CTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGGCAT
        69
        23115475
        0.1861%
        GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGA
        69
        19054746
        0.1534%
        CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGG
        69
        19161758
        0.1543%
        GTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGAT
        69
        16405491
        0.1321%
        CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGG
        69
        16622625
        0.1338%
        GGTCGACCCGTGCGGAGGAGCGAGGAGGAAGGACGCGCGAGGGCCGGGAC
        68
        13200635
        0.1063%
        GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGA
        68
        16259490
        0.1309%
        TCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGAT
        67
        13121142
        0.1056%
        GTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGAT
        67
        14414668
        0.1161%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.12.1